After the storm clears
by dark-nexus17
Summary: What happens after the third film. Smith has gone and Neo is still plugged into the Matrix due to the machines in 01. What will the Matrix be like now that there is peace?
1. Prologue

This is my first fanfic on here, so please R + R. I don't own any of the characters, although I really wish I did.

Time meant nothing to Neo anymore. He did not know how long he had been plugged in; just that he was. He knew he had defeated Smith; had become one of him and been altered by the Matrix. He knew he had stopped the war, and that Trinity was dead. He also knew, he was dying. The light was fading from before his eyes, slowly, but surely. He did not care that he was dying, he longed for it, longed to be where ever Trinity was now.

* * *

Meanwhile, the machines were frantic, the Matrix was whole again, the 'equation' balanced, but the One, whom they still needed, was dying. Although they're knowledge of the human body was advanced, they could find no cause. Within the Matrix, things, exiles, bad programming, unchecked code, began slipping through the cracks, already appearing because of Neo's death. They worked frantically, searching for the answer that would save the humans and themselves further problems.


	2. The beginning of the aftermath

So. First chapter. Time to get into the real story. The aftermath begins.

Neo felt his surroundings change. He was in a room walled with television screens. Vaguely, he knew this room, but he certainly didn't care where he was.

"You are dying." a clipped tone said from somewhere above Neo. He pushed himself into a sitting position.

"I know." he replied, looking into the features of the Architect, who looked uncomfortable.

"We do not know why." said the Architect, a trace of frustration in his voice.

"I do," said another voice, a pleasant, female one. Neo turned to see the Oracle, smiling kindly at him. "He is dying because he has no purpose now."

"But he is the One." growled the Architect. "He exists to balance the equation, to save the Matrix."

"That does not matter." said the Oracle sadly. "He is dying because Trinity is dead."

"Ah," murmured the Architect, "His 'lover'."

Neo watched the Architect as he looked at the TV screens, where Trinity's last moments in the real world were being displayed, Neo looked away after a few seconds, he could not bear to watch Trinity die again.

After a moment, the screens went blank. The Architect turned to Neo, and pursed his lips.

"She has been dead less than an hour," he told Neo, "I will send machines to bring her back to the source. We can heal her." he continued, "But at a cost."

"He will do anything." the Oracle said to the Architect, looking fondly at Neo, who listened, unbelievingly. He forced himself to speak.

"You cannot violate the peace treaty." he said quietly. "But I will do anything else you ask." He submitted himself, bowing his head.

The Architect deliberated for a moment, as if choosing his words carefully.

"You must be our messenger to Zion." he finally told Neo. You must tell them that some humans must remain plugged in, until we can find a suitable alternative energy source."

"I will do it." Neo promised.

"Trinity is now in 01." the Oracle said after a pause in the conversation. "As soon as she is healed enough to travel, you must return in the ship you came. It has been fixed." she smiled at him. "Don't stay away for too long Neo. I've missed our talks."


	3. The return

Chapter 2 – The return

Neo awoke to darkness, apart from the glow of the machines. He was cold, so cold, but he knew he had to get up; he had a sense of purpose now. As he struggled to his feet, a voice like thunder spoke, it was the Source.

"It is done," said the voice. "Don't forget your promises."

The voice faded into the whir of a million machine parts. Then another voice called him.

"Neo," said Trinity quietly. He could not see her. He dropped to his knees and crawled towards the sound of her voice. Eventually he found her. Her warm body, restored to him.

"Trinity," he murmured.

"Am I still dead?" she asked, her voice wavering. "Did you die? Is the war over?"

Neo began to sob; he was so grateful that they were both alive. He was overwhelmed.

"Trin," he managed to choke out after a while, "We're alive, I'm afraid you're still a bit hurt, but you're alive, and the war – the war is over. We have to go back to Zion."

"But, I died." Trinity said, more certain now.

"Yes," sobbed Neo, "I nearly did too, but I've made a deal with the machines – with the Oracle and the Architect – they brought you back. I couldn't let go."

Trinity did not ask what the deal was, but comforted him instead.

"Shh," she whispered gently, "It's okay." She looked around then, and saw the Logos, not far off. "Come on," she said. "We need to get back." She took his hand and helped him slowly to his feet, she gasped when she saw his still ruined eyes. "Looks like I'm driving again." she said dryly.

"This is the Logos, requesting entrance through gate 4," Trinity said hoarsely into the ship's communication device.

"The Logos?" a young male voice asked, he sounded both shocked and disbelieving, "We thought the Logos was missing …" he broke of suddenly, and a calm, assured voice spoke next, one that brought tears to Trinity's eyes. _Thank God. _She thought.

"Welcome home Trinity." Morpheus said.

The gate opened slowly, and Trinity carefully guided the ship through the small passage and into the savaged docking space, that was barely holding together. She looked down at Neo, who, exhausted, had fallen asleep on the way. He was holding her hand.

"Neo," she said. His eyelids fluttered open.

"Trin," he said groggily, "Where are we?"

"Home." She whispered as the door opened, and Morpheus and Niobe came aboard.

She smiled. And then collapsed.


	4. Recovery

Chapter 3 – Recovery

Neo held Trinity's hand as she lay in her white hospital bed. He heard her slow, steady breathing as she slept peacefully. Her operation had been long, too long, as the doctors repaired the rest of the damage to her body, but it had been successful. He himself had not rested since they arrived. He fought the immense weariness, knowing that he would have to succumb sooner or later. He raised his head as he heard footsteps.

"Rest Neo." It was Morpheus, come to check on Trinity. He was not surprised to find Neo there. "Trinity will be fine" He said.

"I must tell the counsel something," Neo said, knowing that the promise he had made to the machines needed to be kept.

"It will wait until tomorrow Neo," Morpheus assured him. "Rest."

Neo gave into the darkness then, and fell asleep in the chair where he sat.

When he awoke he was in a bed of his own. He could feel the cool, crisp sheets on top of him. Odd, he had not been woken whilst being moved. He raised his head slightly from the pillow. He could hear, muffled sounds, footsteps, a rhythmic beeping, and the sound of someone breathing nearby. A slight pressure on his head made him reach upwards, he could feel a bandage, he grasped it, intending to take it off.

"The doctors said you had to keep that on." Trinity said, close by.

Neo sat up quickly, reaching for her, blood rushed to his head, and he had to lie down again. He waited for a minute, and then said,

" Trinity. You're awake? How are you? How long have I been here? Are you…" Trinity interrupted his rush of panicked words.

"Shh, Neo. Shh. I'm fine." She came to sit on his bed, and hugged him gently, as if he was the one who had received multiple puncture wounds. She bent down and kissed him softly.

"I'm so glad you're okay." Neo said.

"Me too Neo, I felt awful leaving you alone in 01." She began to sob quietly, this frightened Neo a little, Trinity had never cried, not even when she had died aboard the Logos. He wrapped his arms around her, and she leaned into him, grateful for the contact.

"We're together now." He murmured into her hair. "It's going to be alright." He hesitated then, before saying "Trin. I love you."

He heard the smile in her voice as she replied, "I love you too Neo."

They sat quietly for a moment, in each other's arms, focusing on the comfort that it brought. Neo broke the silence.

"Trin," he said. "My eyes. Are they…?" he trailed off, not wanted to finish the question.

"They should be okay." Trinity replied. "The skin around them still need time to heal, but they managed to correct your sight. It will hurt for a while though." She told him.

"I feel so useless." He admitted. "I can't even see you." Trinity could hear the ache in his voice, and see it on his face.

"You're not useless." She said sharply. "Besides, you can still see in the Matrix."

"How did you know that?" Neo asked

"You were muttering in your sleep," Trinity said. "Me and Morpheus managed to piece together most of what happened. You need to see the council, right?"

"Yes," Neo said, "I need to tell them about the machines, and at some point, soon, I need to go back into the Matrix."

"You can't!" Trinity said loudly, startling him. "It's too dangerous, and you need to rest."

"Trin," said Neo softly. "I must. I promised the Oracle." He sighed. "I won't go in for a couple of weeks at least." He told her, "There's so much to sort out."

Trinity was silent as she calmed herself down.

"Okay Neo." She said finally, "If that's what you want."

"It's what I promised," he said. He paused for a moment, "Trin, I'm sorry, it's a lot to take in, you must be tired. Go to bed and rest."

"I want to stay with you." Trinity said quietly, as if she expected rejection.

"Get in bed with me then." Neo said, moving over slightly, trying to gauge where the edge of the bed was. Trinity slithered under the covers and wrapped her arms around him. She was asleep within minutes.

"I love you so much Trin." Neo said to her sleeping form. "Don't leave me again." He


End file.
